MiR-CLIP

MiR-CLIP

miR-CLIP was developed to identify mRNA targets of miRNA, using synthetic miRNAs. The capture probes in miR-CLIP are pre-miRNAs conjugated to psoralen and biotin that can be crosslinked with mRNA to isolate their targets from total RNA.

First, a miR-CLIP capture probe needs to be designed and tested for functionality and strong binding affinity. Next, they are transfected into cells and UV-crosslinked at 254 nm and 365 nm, followed by immunoprecipitation of the crosslinked complex. The RNA is extracted and further purified by streptavidin pull-down. The isolated RNA targets can now be reverse-transcribed and processed into cDNA libraries for sequencing.

Pros:

• Identifies targets of miRNAs genome-wide
• Capture probe miRNA sequence can be easily modified to investigate different miRNA species

Cons:

• Not yet widely adapted by the scientific community
• Requires careful design of miRNA capture probes

• MiR-CLIP: Imig J., Brunschweiger A., Brummer A., Guennewig B., Mittal N., et al. (2014) miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nat Chem Biol advance online publication:

1. Sandhu G. K., Milevskiy M. J. G., Wilson W., Shewan A. M. and Brown M. A. Non-coding RNAs in Mammary Gland Development and Disease. Non-coding RNA and the Reproductive System. 2016;121-153
2. Yu B. and Shan G. Functions of long noncoding RNAs in the nucleus. Nucleus. 2016;7:155-166
3. Jeker L. T. and Marone R. Targeting microRNAs for immunomodulation. Curr Opin Pharmacol. 2015;23:25-31
4. Tycowski K. T., Guo Y. E., Lee N., et al. Viral noncoding RNAs: more surprises. Genes Dev. 2015;29:567-584

1. Imig J., Brunschweiger A., Brummer A., et al. miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nat Chem Biol. 2014;advance online publication: